Contacts of the helix formed by residues 463 - 471 (chain N) in PDB entry 3FKS
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ILE 463 (chain N).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413N PHE* 4.1 7.4 - - + -
436N ASP* 4.0 5.3 + - - +
439N ALA 5.8 0.4 - - - -
440N SER* 3.1 45.7 + - - +
443N ALA* 5.5 3.4 - - + -
444N VAL* 5.4 5.2 - - + -
449N TYR* 3.7 40.6 - - + +
457N PHE* 6.6 0.2 - - + -
462N GLY* 1.3 70.8 - - - -
464N GLU* 1.3 90.7 + - + +
465N ASP 3.2 1.6 - - - -
466N VAL* 3.2 23.3 + - + +
467N VAL* 3.9 6.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 464 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436N ASP* 3.4 32.0 - - - +
462N GLY* 4.2 3.1 - - - -
463N ILE* 1.3 92.0 + - + +
465N ASP* 1.3 68.6 + - - +
466N VAL 3.0 1.4 + - - -
467N VAL* 3.3 17.1 + - - +
468N ALA* 3.4 11.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 465 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430N LYS* 4.1 22.7 - - - +
460N VAL* 4.5 8.4 - - + +
461N GLY* 4.0 25.0 + - - +
462N GLY* 4.0 17.4 + - - +
463N ILE 3.2 0.6 - - - -
464N GLU* 1.3 86.0 - - - +
466N VAL* 1.3 60.5 + - - +
468N ALA* 3.7 10.2 + - - +
469N LYS* 3.2 21.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 466 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413N PHE* 3.4 32.5 - - + -
449N TYR* 6.0 1.8 - - + -
452N ILE* 4.5 9.2 - - + -
456N ALA* 3.4 28.2 - - + +
457N PHE* 3.8 27.1 - - + -
460N VAL* 4.0 7.9 - - + -
462N GLY 3.5 7.0 - - - +
463N ILE* 3.3 20.4 - - + +
464N GLU 3.0 0.6 - - - -
465N ASP* 1.3 77.0 - - - +
467N VAL* 1.3 56.3 + - + +
469N LYS* 3.1 3.8 + - - +
470N ALA* 2.8 33.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 467 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449N TYR* 4.2 26.2 - - + +
452N ILE* 4.6 9.2 - - + -
463N ILE* 4.2 12.3 - - + +
464N GLU* 3.3 8.6 + - - +
466N VAL* 1.3 75.7 - - + +
468N ALA* 1.3 63.4 + - - +
470N ALA* 3.6 7.1 - - + +
471N GLU* 3.2 34.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 468 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464N GLU 3.4 8.7 + - - +
465N ASP* 3.8 12.3 - - - +
466N VAL 3.2 0.4 - - - -
467N VAL* 1.3 79.8 - - - +
469N LYS* 1.3 58.0 + - - +
471N GLU* 3.6 13.9 - - - +
472N LYS* 3.0 40.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 469 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455N HIS* 3.5 28.3 + - - -
456N ALA* 3.6 24.2 - - + +
458N TYR* 2.9 30.7 + - - +
459N MET* 4.3 3.8 + - - +
460N VAL* 3.6 11.9 - - + +
465N ASP 3.2 11.5 + - - +
466N VAL 3.1 8.4 + - - +
468N ALA* 1.3 79.6 - - - +
470N ALA* 1.3 65.8 + - - +
472N LYS* 3.2 18.6 + - + +
473N LEU* 3.3 10.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 470 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452N ILE* 3.5 35.7 - - + -
453N PRO* 5.0 6.9 - - + +
456N ALA* 4.2 8.2 - - - +
466N VAL 2.8 15.5 + - - +
467N VAL* 3.2 10.5 + - + +
469N LYS* 1.3 77.0 - - - +
471N GLU* 1.3 57.9 + - - +
472N LYS 3.0 0.2 - - - -
473N LEU* 3.0 29.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 471 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467N VAL* 3.2 23.8 + - + +
468N ALA* 3.6 15.1 - - - +
470N ALA* 1.3 78.8 - - - +
472N LYS* 1.3 63.0 + - + +
473N LEU 3.2 7.3 + - - +
474N ALA* 5.8 0.7 - - - +
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il